Master Bra'tac arrives with bad news: Teal'c's wife is deathly ill, and Teal'c leaves to be with her. Shortly thereafter, the gate is opened but nothing comes through. Then Carter discovers a very low power signal that is slowly building an overload powerful enough to destroy the Earth.

Anubis' weapon continues to threaten Earth. Various plans are tried until Jonas Quinn suggests something simple that just might work. Meanwhile, Master Bra'tac has discovered the planet from which Anubis is launching the attack. He, Teal'c and Rya'c journey there to put a stop to it.

Stargate Command discovers a Goa'uld Ha'tak in Earth orbit. Exploring, they discover it is the ship where Anubis briefly imprisoned Thor. At some point, Anubis' forces set the self-destruct and abandoned the ship, but something has halted the destruction and brought the ship to Earth. Jacob/Selmak opens the computer core so the team may learn more. Then the ship begins to descend towards Earth. SG-1 must discover what's going on before the destruction of the Ha'tak threatens Earth. And hopefully, escape the doomed ship themselves.

A team associated with Stargate Command and posted in Antarctica makes an astounding discovery - a perfectly preserved, apparently human woman who has been frozen since the Antarctic Stargate was first deployed. Then they discover she is still alive, and work to revive her. But her revival costs the team: they and SG-1 succumb to a deadly disease the woman apparently carries. She can save them but not herself. And the effort exhausts her; she may not be able to save everyone before the disease claims her life.

A scientist named Fleming contacts SG-1. It seems the work of Immunotech has not stopped. The investigation carries SG-1 to a town in Oregon whose citizens lead curious double lives - right under the watchful eye of the NID. But all is not as it appears in a number of ways, and SG-1 must work quickly to prevent the NID's secret project from becoming a disaster for Earth.

Healed after being nearly killed by an Ancient virus, O'Neill finds himself held captive on a planet controlled by the Goa'uld Ba'al. O'Neill was brought here by the Tok'Ra symbiote that healed him and Ba'al wants to know why. When O'Neill can not give him an answer, he soon finds himself being tortured by Ba'al. As Carter, Teal'c and Jonas Quinn attempt to go through the Tok'ra records to find out where O'Neill was sent by the symbiotic, O'Neill is killed and brought back to life many times by Ba'al and his only hope to keep his sanity comes in the form of the ascended Daniel Jackson.

Jonas Quinn's mentor, Dr. Keiran, visits Earth with the leader of Kelowna and an ambassador. Tensions are escalating and they see no alternative but to build and use a nahquadria bomb - a weapon of cataclysmic effect and long term consequence. Stargate Command is faced with giving them superior weapons or "forcing" them to use a deadly device. But Dr. Keiran might have an alternative - a mysterious underground only he can contact who can overthrow the government and bring peace - if that government doesn't find them first, and if Keiran is telling the truth...

Told from the point of view of a stereo-typical scientist, Jay Felger (in love with SG-1). While on a standard science "baby-sitting" mission, SG-1 is captured by Khonsu (who is secretly Tok'Ra) in order to relay information about Anubis. Felger and fellow scientist, Simon Coombs disobey O'Neill's order to return to SGC and sneak onto Khonsu's ship. Khonsu's head Jaffa, Her'ak turns on Khonsu and kills him, keeping SG-1 to turn over to Anubis in the process. Felger and Coombs, manage to help SG-1 escape and return to the SGC.

The Tok'ra are forced to evacuate their newly established base under attack from the Goa'uld. They flee to the SGC's Alpha site. Tensions rise between the allied factions, the Free Jaffa, Tau'ri, and Tok'ra. Jacob and Selmac feel the end of the Tok'ra is near and Sam finds a Naquadah generator has been sabotaged to function as a bomb. Jack suspects the recently arrived Tok'ra and attempts to weed out the traitor.

SG-1 is negotiating a treaty with the inhabitants of Pangera. The have sometime miraculous to offer - a drug they call tretonin that can cure any ill. But there is a catch: the drug replaces the the user's immune system and must be taken forever. The Pangerans want specific world coordinates in exchange for the drug - and some of those places are the homes of powerful system lords. They won't explain why, but it clearly has to do with tretonin. Then the Tok'ra, called in to help solve the problem, make a startling discovery about the ultimate source of tretonin.

A television news crew has unearthed information about an Air Force project called "Prometheus". They believe it to be a generator, but know it uses Trinium, an element not found on Earth. In order to keep them quiet the Air Force allows them to film the X-303, a spaceship based on Asgard technologies, otherwise known as Prometheus. Things turn south when the news crew arm themselves and hold the Prometheus, as well as Sam and Jonas, hostage.

The Asguard home galaxy has been over-run by the replicators, and they ask for SG-1's help. The Asguard believed they had trapped the replicators with a device that would slow down time, but it seems to have failed. They need SG-1 to enter replicator infested space, find the time dilation machine and reset it. When SG-1 land at the designated point, they meet 5 individuals, who control the replicators. The others reveal that they are an evolution of the replicators - composed of micro-cellular replicator blocks, and modeled on Reese, who created the original replicators. These others have reset the time machine so that time is moving more quickly within this area of space - to allow them to evolve and build an enormous army that can invade the rest of space. The minds of the team are probed by the first 4 others. However, the last member of the others (called Fifth) seems reluctant - he is described as weak by First, the leader of the replicators. He was an attempt to model Reese more fully, but the mistake will not be repeated. Carter senses his reluctance to probe her mind, but invites him to do so - and they agree a plan. Fifth will reset the time dilation machine to run slowly, and he will escape with the SG team. While time is passing slowly for his brethren, the Asguard will have hundreds of years to fix the mistake in the others. Fifth has to leave later than the SG team to avoid arousing the suspicion of the others; Jack orders Carter to set the timer on the device to activate earlier than Fifth has been told. SG-1 escape successfully as the time dilation device reverses the trend within the area of space, and makes time run much more slowly. However, Fifth is caught by his brethren, and realises that Carter had broken her promise not to leave without him. Carter and Jonas regret using Fifth's humanity against him, but even though Jack seems uncomfortable, he declares that Fifth wasn't human, and they made the only correct choice.

SG-1 brings back an Ancient device, the purpose of which is unknown. When Jonas touched it the device activated. Upon reaching the SGC Jonas sees a large red insect fly into a wall, but no one else can confirm his sighting. The SGC is put into lockdown, but nothing is found. Jonas suspects that the Ancient device is causing his hallucinations, but to his dismay it is set to be shipped to Area 51. When Teal'c and Jack see the bugs as well, General Hammond decides to let Jonas take a crack at deciphering the Ancient text on the device.

Senator Kinsey is shot in the chest at a public event, killing him just before his party's presidential nomination. Jack is arrested for the murder, and General Hammond assigns the rest of SG-1 to uncover the truth.

Former Colonel Harry Maybourne comes to Jack with a proposition: Jack gets him a presidential pardon and Harry shows them the advanced weapons cache that Simmons was trying to get to. They go through with the deal, but Harry attempts to double cross SG-1. He manages to get through the portal leading to the cache, but with one unexpected item, Jack. They find themselves in a field and Harry's zat is missing. Jack, however, still has his P-90. Harry reveals that they are not at a weapons cache, but rather a utopia. He meant to live out the rest of his life there and believes that there is no way back.

The Russian SG team brings back a man who claims that his people are being experimented on by Nirrti. SG-1 investigate where the experiments are conducted, with the Russian SG team as backup. The inhabitants worship Nirrti as their god and savior from a terrible plague. SG-1 attempts to use the same device Nirrti used on the people to reverse the mutations, but the people turn on them at the arrival of Nirrti.

Ambassadors from a number of world powers have gathered to hear a revelation. Major Davis and General Hammond reveal the existence of the Stargate program. This meeting was engineered in part by Senator Kinsey; it's a political play that could leave him in control of the Stargate program through his flunkies at the NID - unless Hammond can call on an old friend for help.

On a mission to observe a nebula, SG-1 finds a crashed ship and its three human survivors. They soon come under fire from an pair of aliens bearing the weapons of the survivors. They repel the attack, but one of the three is wounded. She is taken to the SGC for treatment while Sam attempts to repair the ship. Jack and Teal'c feel that there is more to the relationship between the aliens and these humans, and attempt to trap an alien.

Teal'c is having strange nightmares featuring Apophis in which he is human and a firefighter with the rest of his team alongside him.

On a shakedown cruise of the Prometheus, the ship's hyperdrive regulator becomes irreparably damaged. A nearby planet was listed on the cartouche of addresses found on Abydos and thus may have a stargate. After a short jump towards the planet, the naquadria reactor overloads and must be jettisoned. After the reactor explodes above the planet causing damage, the fate of SG-1 and the crew of the Prometheus is in the hands of a once Goa'uld-controlled world that they're off to a rough start with.

On a routine mission, SG-1 encounters a civilization desperate to be freed from the clutches of a Goa'uld. While on the planet, Jonas falls ill and is suspended from active duty. His mysterious illness is diagnosed as a brain tumor but gives him the unbelievable ability to glimpse the future, a future where O'Neill and SG-1 are walking into a trap!

With Anubis heading to Abydos looking for a valuable artifact known as the eye of Ra, ascended Daniel Jackson contacts Colonel O'Neill and the rest of SG-1 to have them go to Abydos and find the eye before Anubis. With the help of Daniel, Jonas and Carter find a secret chamber where the eye is kept but not before O'Neill, Teal'c, Skaara, and a group of defenders are overrun and trapped inside the pyramid housing the stargate. But Daniel also finds a tablet, written in ancient, suggesting that there is an Ancient city, lost for thousands of years, that give Earth weapons with which to defeat Anubis. But the only way to get the tablet back to Earth for further translation and for the search for the lost city may be Daniel breaking the high rule of ascension and to destroy Anubis. If he doesn't, Abydos will be destroyed.